LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 50.0% methanol mole fraction solution
# with 2500 methanol molecules in implicit water.
#
#
# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
#
# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)


# Initialize simulation box
dimension       3
boundary        p p p
units           real
atom_style      molecular

# Set potential styles
pair_style      hybrid/overlay table spline 500 local/density

# Read molecule data and set initial velocities
read_data       methanol_implicit_water.data
Reading data file ...
  orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2500 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.016 seconds
velocity        all create  3.0000e+02 12142 rot yes dist gaussian

# Assign potentials
pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 254 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairMM to re-computed values (src/pair_table.cpp:473)
pair_coeff          *     * local/density methanol_implicit_water.localdensity.table




#Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box

#Thermostat & time integration
timestep        1.0
thermo          100
thermo_style    custom etotal ke pe temp evdwl

#minimization
minimize        1.e-4 0.0 1000 1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair_style  local/density  command:

@Article{Sanyal16,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
 journal = {J.~Chem.~Phys.},
 year =    2016,
 DOI = doi.org/10.1063/1.4958629}

@Article{Sanyal18,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
 journal = {J.~Phys.~Chem. B},
 year =    2018,
 DOI = doi.org/10.1021/acs.jpcb.7b12446}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 17
  ghost atom cutoff = 17
  binsize = 8.5, bins = 8 8 8
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair table, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) pair local/density, perpetual, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 9.535 | 9.535 | 9.535 Mbytes
TotEng KinEng PotEng Temp E_vdwl 
   1283.8556    2234.7133   -950.85771          300   -950.85771 
  -10.187232    2234.7133   -2244.9005          300   -2244.9005 
  -124.79406    2234.7133   -2359.5074          300   -2359.5074 
   -126.7619    2234.7133   -2361.4752          300   -2361.4752 
Loop time of 3.74581 on 1 procs for 205 steps with 2500 atoms

99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
     -950.857712502514  -2361.24417962983  -2361.47519428972
  Force two-norm initial, final = 135.25170 2.8038329
  Force max component initial, final = 14.083102 1.1154133
  Final line search alpha, max atom move = 0.16981022 0.18940857
  Iterations, force evaluations = 205 223

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.5678     | 3.5678     | 3.5678     |   0.0 | 95.25
Bond    | 7.5831e-05 | 7.5831e-05 | 7.5831e-05 |   0.0 |  0.00
Neigh   | 0.12962    | 0.12962    | 0.12962    |   0.0 |  3.46
Comm    | 0.019204   | 0.019204   | 0.019204   |   0.0 |  0.51
Output  | 0.00023948 | 0.00023948 | 0.00023948 |   0.0 |  0.01
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.02886    |            |       |  0.77

Nlocal:        2500.00 ave        2500 max        2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6729.00 ave        6729 max        6729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        265637.0 ave      265637 max      265637 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 265637
Ave neighs/atom = 106.25480
Ave special neighs/atom = 0.0000000
Neighbor list builds = 11
Dangerous builds = 0

#set up integration parameters
fix             timeintegration all nve
fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915

#Equilibration (for realistic results, run for 2000000  steps)
reset_timestep  0
thermo          200
thermo_style    custom etotal ke pe temp evdwl

#run equilibration
run             2000
  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 8.410 | 8.410 | 8.410 Mbytes
TotEng KinEng PotEng Temp E_vdwl 
   -126.7619    2234.7133   -2361.4752          300   -2361.4752 
   517.05047    2015.8636   -1498.8131    270.62043   -1498.8131 
   931.78263    2135.4332   -1203.6506     286.6721   -1203.6506 
   1162.6209    2242.1662   -1079.5453    301.00051   -1079.5453 
   1164.2129    2211.6204   -1047.4075    296.89989   -1047.4075 
   1258.0085    2286.5942   -1028.5857    306.96477   -1028.5857 
   1231.1937     2200.814   -969.62032    295.44917   -969.62032 
   1251.2144    2245.0533   -993.83885     301.3881   -993.83885 
   1237.2495    2239.8802   -1002.6307    300.69363   -1002.6307 
   1232.3342    2224.3415   -992.00722    298.60763   -992.00722 
   1235.3228     2197.191   -961.86817     294.9628   -961.86817 
Loop time of 23.6478 on 1 procs for 2000 steps with 2500 atoms

Performance: 7.307 ns/day, 3.284 hours/ns, 84.575 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 22.797     | 22.797     | 22.797     |   0.0 | 96.40
Bond    | 0.00070412 | 0.00070412 | 0.00070412 |   0.0 |  0.00
Neigh   | 0.2249     | 0.2249     | 0.2249     |   0.0 |  0.95
Comm    | 0.12259    | 0.12259    | 0.12259    |   0.0 |  0.52
Output  | 0.00088925 | 0.00088925 | 0.00088925 |   0.0 |  0.00
Modify  | 0.46447    | 0.46447    | 0.46447    |   0.0 |  1.96
Other   |            | 0.03711    |            |       |  0.16

Nlocal:        2500.00 ave        2500 max        2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6752.00 ave        6752 max        6752 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        265940.0 ave      265940 max      265940 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 265940
Ave neighs/atom = 106.37600
Ave special neighs/atom = 0.0000000
Neighbor list builds = 20
Dangerous builds = 0

#turn off recentering during production run
unfix recentering


#setup trajectory output
dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
dump_modify     myDump element M
dump_modify     myDump sort id

#run production (for realistic results, run for 10000000 steps)
reset_timestep  0
thermo          1000
thermo_style    custom etotal ke pe temp  evdwl
run             10000
  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.918 | 9.918 | 9.918 Mbytes
TotEng KinEng PotEng Temp E_vdwl 
   1235.3228     2197.191   -961.86817     294.9628   -961.86817 
   1289.8463    2236.1425   -946.29622    300.19186   -946.29622 
   1348.0825    2305.0295   -956.94703    309.43963   -956.94703 
   1279.5478    2241.1582   -961.61041    300.86521   -961.61041 
   1231.8597    2201.9591   -970.09949    295.60291   -970.09949 
   1277.3424    2221.3696   -944.02725    298.20867   -944.02725 
   1296.0116    2222.0998   -926.08818     298.3067   -926.08818 
   1266.2849    2206.3727   -940.08782     296.1954   -940.08782 
   1313.2808    2260.5077   -947.22683    303.46278   -947.22683 
   1309.3076    2234.3895   -925.08198    299.95654   -925.08198 
   1275.9792    2221.3037   -945.32449    298.19982   -945.32449 
Loop time of 67.3224 on 1 procs for 10000 steps with 2500 atoms

Performance: 12.834 ns/day, 1.870 hours/ns, 148.539 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 64.476     | 64.476     | 64.476     |   0.0 | 95.77
Bond    | 0.0014504  | 0.0014504  | 0.0014504  |   0.0 |  0.00
Neigh   | 0.71333    | 0.71333    | 0.71333    |   0.0 |  1.06
Comm    | 0.32846    | 0.32846    | 0.32846    |   0.0 |  0.49
Output  | 0.46997    | 0.46997    | 0.46997    |   0.0 |  0.70
Modify  | 1.2336     | 1.2336     | 1.2336     |   0.0 |  1.83
Other   |            | 0.09996    |            |       |  0.15

Nlocal:        2500.00 ave        2500 max        2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        6662.00 ave        6662 max        6662 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        265774.0 ave      265774 max      265774 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 265774
Ave neighs/atom = 106.30960
Ave special neighs/atom = 0.0000000
Neighbor list builds = 104
Dangerous builds = 0


Total wall time: 0:01:34
